[Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

[Vincent Carey]

I found
```
<UnsatisfiedLinkError/LinkageError/Error/Throwable/Object/Exception/error/condition>
Error in `toSBGN(system.file("extdata",
"biopax3-short-metabolic-pathway.owl",
    package = "paxtoolsr"), outFile)`: java.lang.UnsatisfiedLinkError:
C:\Program Files\Java\jre1.8.0_311\bin\awt.dll: Can't find dependent
libraries

[ FAIL 1 | WARN 1 | SKIP 3 | PASS 58 ]
```
on a pretty stock windows install on azure.

Now it is a little bleeding edge, but maybe you could  comment on this
error?


R Under development (unstable) (2021-10-19 r81074 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United
States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.utf8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rcmdcheck_1.4.0

loaded via a namespace (and not attached):
 [1] ps_1.6.0                 prettyunits_1.1.1        digest_0.6.28
     crayon_1.4.1             withr_2.4.2
 [6] rprojroot_2.0.2          R6_2.5.1                 cli_3.0.1
     curl_4.3.2               callr_3.7.0
[11] desc_1.4.0               tools_4.2.0              compiler_4.2.0
    processx_3.5.2           pkgbuild_1.2.0
[16] xopen_1.0.0              BiocManager_1.30.16.1001


On Fri, Oct 22, 2021 at 12:25 PM Augustin Luna <cannin using gmail.com> wrote:

> Thanks for the responses. But they are not addressing my problem. I
> have GitHub Actions checking the package on Windows/macOS/Linux using
> Java OpenJDK 14 with tests/examples running fine on both R release and
> devel.
>
> https://github.com/BioPAX/paxtoolsr/actions/runs/1372348962
>
> At this point, I'm not debugging my code rather the Bioconductor build
> system. Tests/examples that do not run on Bioconductor are running
> fine elsewhere.
>
> More helpful to me would be instructions to some VM file or Docker
> container where I could mimic the Bioconductor setup. I'm at a loss
> for how to debug this problem or what is unique about the Bioconductor
> system.
>
> Searching through code from other packages is not helpful unless I
> know what I'm looking for. In this case, it means a package that had a
> "JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote"
> error and addressed it successfully.
>
> Stack Overflow only gives me hints regarding
> "CFMessagePortCreateRemote" errors in that there is a problem with the
> installation of Java:
>
>
> https://stackoverflow.com/questions/15289059/install-java-on-mac-osx-10-8-2-error-calling-cfmessageportcreateremote
>
> PS: I removed the "which java" call.
>
> Thanks,
> Augustin Luna
>
> On Mon, Oct 18, 2021 at 3:14 PM Hervé Pagès <hpages.on.github using gmail.com>
> wrote:
> >
> > Hi Augustin,
> >
> > Please don't rely on JAVA_HOME to detect Java. The JDK installer on
> > Windows doesn't set this variable so you shouldn't expect it to be set
> > on the user's machine. AFAIK the other Bioconductor packages that depend
> > on Java don't use their own code to detect Java. Instead I believe that
> > they run their Java code via rJava so they delegate to rJava the
> > responsibility to find Java for them.
> >
> > Here is the list of all Bioconductor packages that depend on rJava:
> >
> >    ArrayExpressHTS
> >    (not supported on Windows)
> >    BridgeDbR
> >
> >    CHRONOS
> >
> >    debCAM
> >
> >    esATAC
> >
> >    gaggle
> >
> >    Onassis
> >
> >    ReQON
> >
> >    RGMQL
> >
> >    rmelting
> >
> >    sarks
> >
> >    SELEX
> >
> >
> > Feel free to take a look at how they handle this.
> >
> > Cheers,
> > H.
> >
> >
> > On 18/10/2021 10:13, Vincent Carey wrote:
> > > That should be fixable.  The build system needs to have a correct
> setting
> > > for JAVA_HOME.  But you have
> > > clearly nonportable code in .onLoad in paxtoolsr.R -- system("which
> java")
> > > ... this should not be
> > > necessary at all, just import rJava.
> > >
> > > On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna <cannin using gmail.com>
> wrote:
> > >
> > >> I have the following error:
> > >>
> > >> "error: JAVA_HOME cannot be determined from the Registry"
> > >>
> > >> for this package:
> > >>
> > >>
> > >>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/paxtoolsr/riesling1-install.html
> > >>
> > >> I have been given assurances that Java is present but given this
> > >> error, I am not so sure and I am unsure how to debug or fix it.
> > >>
> > >> Can anyone suggest how to proceed?
> > >>
> > >> Thanks,
> > >> Augustin Luna
> > >>
> > >> _______________________________________________
> > >> Bioc-devel using r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.github using gmail.com
>

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